/***************************************************************************
 *   Copyright (C) 2007 by Alexandre Masselot,,,   *
 *   alex@alex-laptop   *
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU Library General Public License as       *
 *   published by the Free Software Foundation; either version 2 of the    *
 *   License, or (at your option) any later version.                       *
 *                                                                         *
 *   This program is distributed in the hope that it will be useful,       *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 *   GNU General Public License for more details.                          *
 *                                                                         *
 *   You should have received a copy of the GNU Library General Public     *
 *   License along with this program; if not, write to the                 *
 *   Free Software Foundation, Inc.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/
#ifndef DBSEQUENCEFACTORYFASTA_H
#define DBSEQUENCEFACTORYFASTA_H

#include "dbsequencefactory.h"
#include <fstream>
#include <string>
#include <boost/regex.hpp>

/**
a DBSequenceFactory based on a fasta input stream

	@author Alexandre Masselot,,, <alex@alex-laptop>
*/
namespace bol{
class DBSequenceFactoryFasta:public DBSequenceFactory{
private:
  istream* m_inputStream;
  string m_nextline;
  boost::regex m_pattern_seqspace, m_pattern_header;
  
public:
    /**
     * 
     */
    DBSequenceFactoryFasta();

    /**
     * 
     */
    ~DBSequenceFactoryFasta();

    /**
     * read the  next sequence
     * @param entry is replace by the newly read data
     * @return true is a seqeunce could be read
     */
    bool nextSequence(DBSequence& entry);

  /**
   * open a file and set it as the source
   * @param filename 
   */
  void openFile(const string filename);

  /**
   * set the inputstream (typically an input file stream)
   */
  void setInputStream(istream* theValue) {
      m_inputStream = theValue;
  }
  

  /**
   * 
   * @return the inout file stream
   */
  istream* inputStream() const {
      return m_inputStream;
  }
  
};
}
#endif
